Dear All - I have prepared a beta distribution of the much awaited biojava 1.5. The source, binaries and docs for the release can be obtained from the biojava site at http://biojava.org/wiki/BioJava:Download
The API docs are also available on line at http://www.biojava.org/docs/api15b/index.html There are significant new features in this release: * biojavax, the biojavax packages are extensions to the basic biojava. They give access to more detailed objects with better functionality. Most useful to the average user will be the new file parsers (see RichSequence.IOTools) and the RichSequence object. See the biojavax docs for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs). * Hibernate interaction with BioSQL. The prefered method of interaction with BioSQL is now via Hibernate. RichSequence and it's associated objects have hibernate mappings to biosql databases. This provides a number of the benefits of Hibernates ORM to biojava, especially control over transactions and the removal of JDBC code. See http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for details. * Genetic Algorithms. A very flexible genetic algorithm library is available in the biojavax packages. Simple examples are at http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much more powerful things are possible. * Several new features are available in the Structure package that allow manipulation of 3D structure files and objects. * Non HMM Implementations of the NW and SW alignment algorithms are now available in the alignment package. * A new package for handling external processes (org.biojava.utils.process). * Dozens of bug fixes. Please take it out for a spin this weekend and let us know how it works. You will probably find it more reliable than biojava-1.4 even though this is technically a beta. Many thanks to all the volunteers who have contributed to biojava! Best regards, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
